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- EMDB-31583: Apo form of human bile salts export pump ABCB11 -

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Basic information

Entry
Database: EMDB / ID: EMD-31583
TitleApo form of human bile salts export pump ABCB11
Map data
Sample
  • Organelle or cellular component: ABCB11
    • Protein or peptide: bile salts export pump
Function / homology
Function and homology information


canalicular bile acid transmembrane transporter activity / positive regulation of bile acid secretion / Defective ABCB11 causes PFIC2 and BRIC2 / canalicular bile acid transport / intracellular canaliculus / xenobiotic export from cell / regulation of fatty acid beta-oxidation / regulation of bile acid metabolic process / ABC-type bile acid transporter activity / bile acid signaling pathway ...canalicular bile acid transmembrane transporter activity / positive regulation of bile acid secretion / Defective ABCB11 causes PFIC2 and BRIC2 / canalicular bile acid transport / intracellular canaliculus / xenobiotic export from cell / regulation of fatty acid beta-oxidation / regulation of bile acid metabolic process / ABC-type bile acid transporter activity / bile acid signaling pathway / bile acid biosynthetic process / xenobiotic transmembrane transport / bile acid transmembrane transporter activity / phospholipid homeostasis / intercellular canaliculus / bile acid metabolic process / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / ABC-type xenobiotic transporter activity / bile acid and bile salt transport / lipid homeostasis / carbohydrate transmembrane transporter activity / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Recycling of bile acids and salts / xenobiotic metabolic process / cholesterol homeostasis / fatty acid metabolic process / response to organic cyclic compound / recycling endosome / transmembrane transport / response to estrogen / recycling endosome membrane / response to ethanol / response to oxidative stress / endosome / protein ubiquitination / apical plasma membrane / Golgi membrane / cell surface / ATP hydrolysis activity / extracellular exosome / ATP binding / membrane / plasma membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Bile salt export pump
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWang L / Hou WT
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Cell Res / Year: 2020
Title: Cryo-EM structure of human bile salts exporter ABCB11.
Authors: Liang Wang / Wen-Tao Hou / Li Chen / Yong-Liang Jiang / Da Xu / Linfeng Sun / Cong-Zhao Zhou / Yuxing Chen /
History
DepositionJul 29, 2021-
SupersessionAug 11, 2021ID: EMD-0956
Header (metadata) releaseAug 11, 2021-
Map releaseAug 11, 2021-
UpdateAug 11, 2021-
Current statusAug 11, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6lr0
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31583.png

Downloads & links

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Map

FileDownload / File: emd_31583.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 216 pix.
= 228.96 Å		1.06 Å/pix.
x 216 pix.
= 228.96 Å		1.06 Å/pix.
x 216 pix.
= 228.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-2.8344681 - 4.5915093
Average (Standard dev.)0.007123214 (±0.098121256)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 228.95999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z228.960228.960228.960
α/β/γ90.00090.00090.000
start NX/NY/NZ594743
NX/NY/NZ375263
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS216216216
D min/max/mean-2.8344.5920.007

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Supplemental data

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Sample components

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Entire : ABCB11

EntireName: ABCB11
Components
  • Organelle or cellular component: ABCB11
    • Protein or peptide: bile salts export pump

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Supramolecule #1: ABCB11

SupramoleculeName: ABCB11 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293

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Macromolecule #1: bile salts export pump

MacromoleculeName: bile salts export pump / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MSDSVILRSI KKFGEENDGF ESDKSYNNDK KSRLQDEKKG DGVRVGFFQL FRFSSSTDIW LMFVGSLCA FLHGIAQPGV LLIFGTMTDV FIDYDVELQE LQIPGKACVN NTIVWTNSSL N QNMTNGTR CGLLNIESEM IKFASYYAGI AVAVLITGYI QICFWVIAAA ...String:
MSDSVILRSI KKFGEENDGF ESDKSYNNDK KSRLQDEKKG DGVRVGFFQL FRFSSSTDIW LMFVGSLCA FLHGIAQPGV LLIFGTMTDV FIDYDVELQE LQIPGKACVN NTIVWTNSSL N QNMTNGTR CGLLNIESEM IKFASYYAGI AVAVLITGYI QICFWVIAAA RQIQKMRKFY FR RIMRMEI GWFDCNSVGE LNTRFSDDIN KINDAIADQM ALFIQRMTST ICGFLLGFFR GWK LTLVII SVSPLIGIGA ATIGLSVSKF TDYELKAYAK AGVVADEVIS SMRTVAAFGG EKRE VERYE KNLVFAQRWG IRKGIVMGFF TGFVWCLIFL CYALAFWYGS TLVLDEGEYT PGTLV QIFL SVIVGALNLG NASPCLEAFA TGRAAATSIF ETIDRKPIID CMSEDGYKLD RIKGEI EFH NVTFHYPSRP EVKILNDLNM VIKPGEMTAL VGPSGAGKST ALQLIQRFYD PCEGMVT VD GHDIRSLNIQ WLRDQIGIVE QEPVLFSTTI AENIRYGRED ATMEDIVQAA KEANAYNF I MDLPQQFDTL VGEGGGQMSG GQKQRVAIAR ALIRNPKILL LDMATSALDN ESEAMVQEV LSKIQHGHTI ISVAHRLSTV RAADTIIGFE HGTAVERGTH EELLERKGVY FTLVTLQSQG NQALNEEDI KDATEDDMLA RTFSRGSYQD SLRASIRQRS KSQLSYLVHE PPLAVVDHKS T YEEDRKDK DIPVQEEVEP APVRRILKFS APEWPYMLVG SVGAAVNGTV TPLYAFLFSQ IL GTFSIPD KEEQRSQING VCLLFVAMGC VSLFTQFLQG YAFAKSGELL TKRLRKFGFR AML GQDIAW FDDLRNSPGA LTTRLATDAS QVQGAAGSQI GMIVNSFTNV TVAMIIAFSF SWKL SLVIL CFFPFLALSG ATQTRMLTGF ASRDKQALEM VGQITNEALS NIRTVAGIGK ERRFI EALE TELEKPFKTA IQKANIYGFC FAFAQCIMFI ANSASYRYGG YLISNEGLHF SYVFRV ISA VVLSATALGR AFSYTPSYAK AKISAARFFQ LLDRQPPISV YNTAGEKWDN FQGKIDF VD CKFTYPSRPD SQVLNGLSVS ISPGQTLAFV GSSGCGKSTS IQLLERFYDP DQGKVMID G HDSKKVNVQF LRSNIGIVSQ EPVLFACSIM DNIKYGDNTK EIPMERVIAA AKQAQLHDF VMSLPEKYET NVGSQGSQLS RGEKQRIAIA RAIVRDPKIL LLDEATSALD TESEKTVQVA LDKAREGRT CIVIAHRLST IQNADIIAVM AQGVVIEKGT HEELMAQKGA YYKLVTTGSP I S

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 385065
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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